We present a sublinear time algorithm for computing a near optimal low-rank approximation to any positive semidefinite (PSD) Toeplitz matrix $T\in \mathbb{R}^{d\times d}$, given noisy access to its entries. In particular, given entrywise query access to $T+E$ for an arbitrary noise matrix $E\in \mathbb{R}^{d\times d}$, integer rank $k\leq d$, and error parameter $δ>0$, our algorithm runs in time $\text{poly}(k,\log(d/δ))$ and outputs (in factored form) a Toeplitz matrix $\widetilde{T} \in \mathbb{R}^{d \times d}$ with rank $\text{poly}(k,\log(d/δ))$ satisfying, for some fixed constant $C$, \begin{equation*} \|T-\widetilde{T}\|_F \leq C \cdot \max\{\|E\|_F,\|T-T_k\|_F\} + δ\cdot \|T\|_F. \end{equation*} Here $\|\cdot \|_F$ is the Frobenius norm and $T_k$ is the best (not necessarily Toeplitz) rank-$k$ approximation to $T$ in the Frobenius norm, given by projecting $T$ onto its top $k$ eigenvectors. Our result has the following applications. When $E = 0$, we obtain the first sublinear time near-relative-error low-rank approximation algorithm for PSD Toeplitz matrices, resolving the main open problem of Kapralov et al. SODA `23, whose algorithm had sublinear query complexity but exponential runtime. Our algorithm can also be applied to approximate the unknown Toeplitz covariance matrix of a multivariate Gaussian distribution, given sample access to this distribution, resolving an open question of Eldar et al. SODA `20. Our algorithm applies sparse Fourier transform techniques to recover a low-rank Toeplitz matrix using its Fourier structure. Our key technical contribution is the first polynomial time algorithm for \emph{discrete time off-grid} sparse Fourier recovery, which may be of independent interest.